The segment statement
generates the molecular structure by interpreting the coordinate
file to obtain the residue
sequence or by explicitly specifying the residue sequence.
The residues have to be
defined in the topology statement (Section 3.1.1). A
segment is
defined as a protein with one continuous polypeptide chain, a
continuous polypeptide chain itself, a substrate, a cofactor,
a ligand, a set of water molecules, or a single nucleic acid strand.
For a
combination of proteins, water, substrates, ligands, and/or nucleic acids,
the
user should first
split the original coordinate file into several files containing the
segments,
generate each segment separately, and, if necessary, apply appropriate
patches to establish covalent links between segments or within segments,
such
as disulfide bridges.